Applied Geochemistry EDA

Documentation for package ‘rgr’ version 1.1.15

DESCRIPTION file.

Help Pages

rgr-1.1.15-package	Geological Survey of Canada Applied Geochemistry EDA
rgr-package	Geological Survey of Canada Applied Geochemistry EDA

-- A --

ad.plot1	Plot Results of Analytical Duplicate Analyses
ad.plot2	Plot Results of Analytical Duplicate Analyses, Alternate Input
ad.plot3	Plot Results of Analytical Duplicate Analyses as Ratios
ad.plot4	Plot Results of Analytical Duplicate Analyses as Ratios, Alternate Input
ad.test	National Geochemical Reconnaissance survey QA/QC data
alr	Additive Log-Ratio (alr) transformation
alts2dups	Create a Matrix of Duplicate Pairs from Sequential Data
anova1	Analysis of Variance (ANOVA)
anova2	Analysis of Variance (ANOVA), Alternate Input

-- B --

bwplots	Plot Vertical Box-and-Whisker Plots
bwplots.by.var	Plot Vertical Box-and-Whisker Plots for Variables
bxplot	Plot a Horizontal Boxplot or Box-and-Whisker Plot

-- C --

caplot	Prepare a Concentration-Area (C-A) Plot
cat2list	Divides Data into Subsets by Factor
clr	Centred Log-Ratio (clr) transformation
cnpplt	Cumulative Normal Percentage Probability (CPP) Plot
crm.plot	Plot Results of Control Reference Material (CRM) Analyses
crm.plot.new	Plot Results of Control Reference Material (CRM) Analyses Adding New Data
crm.test	National Geochemical Reconnaissance survey QA/QC data
crm.test.new	Simulated National Geochemical Reconnaissance survey QA/QC data
cutter	Function to Identify in Which Interval a Value Falls

-- D --

df.test	Check for the Existence of a Data Frame
display.ascii.o	Display the Windows Latin 1 Font Octal Table
display.lty	Display Available Line Styles and Colour Codes
display.marks	Display Available Plotting Marks
display.rainbow	Display the Colours of the Rainbow(36) Pallette

-- E --

expit

Inverse-logit transformation(s)

-- F --

fences	Generate and Display Fence Values
fences.summary	Generate and Save Fence Values for Data Subsets
fix.test	Test Data for Function ltdl.fix.df
fix.test.asis	Test Data for Function ltdl.fix.df
framework.stats	Compile Framework/Subset Summary Statistics
framework.summary	Generate and Save Framework/Subset Summary Statistics

-- G --

gx.2dproj	Function to Compute and Display 2-d Projections for Data Matrices
gx.2dproj.plot	Function to Display a Saved 2-d Projection Object
gx.add.chisq	Function to Add Fences to Chi-square Plots
gx.adjr2	Function to compute Adjusted r-squared values
gx.cnpplts	Multiple (max 9) Cumulative Normal Probability (CPP) plots
gx.cnpplts.setup	Set Up and Display Symbolgy for function 'gx.cnpplts'
gx.eb	Computation of Empirical Balances
gx.ecdf	Emprical Cumulative Distribution Function (ECDF)
gx.fractile	Estimate the Fractile for a Specified Quantile
gx.hist	Plot a Histogram
gx.hypergeom	Compute Probabilities for Target Recognition
gx.ilr	Isometric Log-Ratio (ilr) transformation
gx.ks.test	Kolmogorov-Smirnov test with ECDF Plot
gx.lm.vif	Estimate Variance Inflation Factosr (VIFs)
gx.md.display	Function to Display Membership Probabilities and Other Relevant Data
gx.md.gait	Function for Multivariate Graphical Adaptive Interactive Trimming
gx.md.gait.closed	Function for Multivariate Graphical Adaptive Interactive Trimming with Compositional Data
gx.md.plot	Function to Display Chi-square Plots of Mahalanobis Distances
gx.md.plt0	Function to Display Chi-square plots of Mahalanobis Distances
gx.md.print	Function to Display Membership Probabilities
gx.mf	Prepare a Concentration-Number (C-N) Plot
gx.mva	Function to undertake an Exploratory Multivariate Data Analysis
gx.mva.closed	Function to undertake an Exploratory Multivariate Data Analysis on Compositional, geochemical data
gx.mvalloc	Function for Allocation on the basis of Multivariate Data
gx.mvalloc.closed	Function for Allocation on the basis of Multivariate Data for closed Compositional Data
gx.mvalloc.print	Function to display the results of Multivariate Allocation
gx.ngr.ltdl	Displays a Count of Negative and Coded Values and NAs for a Data Frame
gx.ngr.skew	Estimate the Skewness of a Data Vector
gx.ngr.stats	Computes Summary Statistics for a NGR Report Table
gx.ngr.summary	Saves a NGR Report Summary Statistics Table to a .csv File
gx.pairs4parts	Display a Graphical Matrix for Parts of a Compositional Data Set
gx.pearson	Display Pearson Correlation Coefficients and their Significances
gx.plot2parts	Display Plots for Two Parts from a Compositional Data Set
gx.quantile	Estimate the Quantile for a Specified Fractile
gx.quantiles	Estimate the Common Quantiles
gx.rma	Estimate the Coefficients of the Reduced Major Axis
gx.robmva	Function to undertake a Robust Exploratory Multivariate Data Analysis
gx.robmva.closed	Function to undertake a Robust Closed Data Multivariate EDA
gx.rotate	Function to Perform a Kaiser Varimax Rotaion
gx.rqpca.loadplot	Function to Graphically Display PCA Loadings
gx.rqpca.plot	Function to Plot Principal Component Analysis Loadings and Scores
gx.rqpca.print	Function to Display PCA Loadings and Scores
gx.rqpca.save	Function to Save PCA Loadings and Scores as .csv files
gx.rqpca.screeplot	Display a Scree Plot
gx.runs	The Wald-Wolfowitz, 'Runs', Test
gx.scores	Function to Compute Scores on the Basis of Threshold Estimates
gx.sm	Display Robust ilr Stabilities and log-ratio Medians for Compositional Data
gx.sort	Function to Single Column Sort a Matrix or Data Frame
gx.sort.df	Function to Multi-Column Sort a Data Frame
gx.spearman	Display Spearman Correlation Coefficients and their Significances
gx.stats	Function to Compute and Display Summary Statistics
gx.subset	Extracts a Subset of Rows from a Data Frame
gx.summary	Compiles a Table of Summary Statistics
gx.summary.groups	Displays Summary Statistics for a Variable Grouped by a Factor
gx.summary.mat	Displays Summary Statistics for a Matrix or Data Frame
gx.summary1	Display a one-line Summary Statistics Report
gx.summary2	Display a ten-line Summary Statistics Report
gx.symm.coords	Computation of Symmetric Coordinates
gx.symm.coords.mat	Create a Matrix of Symmetric Coordinates
gx.symm.coords.plot	Display a X-Y Plot, Scatterplot, of Symmetric Balances
gx.symm.coords.r	Displays a Matrix of Correlation Coefficients based on Symmetric Balances
gx.t.test	t-test from Means, Standard Deviations and Sample Sizes
gx.triples.aov	Carries out a 3-Level Staggered ANOVA and Estimates Variance Components
gx.triples.fgx	ANOVA to Estimate if 'Triples' are a Valid Subset
gx.vm	Display an Aitchison Variation Matrix for Compositional Data
gx.youden	Estimate the Coefficients of the Reduced Major Axis

-- I --

ilr	Isometric Log-Ratio (ilr) transformation
ilr.stab	Compute the Robust ilr Stability for Two Parts of a Composition
inset	An EDA Graphical and Statistical Summary
inset.exporter	Saves an EDA Graphical and Statistical Summary

-- K --

kola.c	Kola Project C-horizon Soil Data
kola.o	Kola Project O-horizon Soil Data

-- L --

logit	Logit transformation
ltdl.fix	Replace Negative Values Representing Less Than Detects in a Vector
ltdl.fix.df	Replace Negative Values Representing Less Than Detects in a Data Frame
ltdl.summary	Displays a Count of Negative and Coded Values and NAs for a Data Frame

-- M --

map.eda7	Plot a Symbol Map of Data Based on the Tukey Boxplot
map.eda8	Plot a Symbol Map of Data Based on their Percentiles
map.tags	Plot a Map of Posted Values
map.z	Plot a Map of Data using Proportional Symbols
ms.data1	Measurement Variability Test Data
ms.data2	Measurement Variability Test Data
ms.data3	Measurement Variability Test Data

-- N --

Nockolds	The Nockolds average igneous plutonic rock compositions
nockolds	The Nockolds average igneous plutonic rock compositions

-- O --

ogrady	Lithogeochemical Data Set from the O'Grady Pluton, NWT, 1970
ogrady.mat2open	Lithogeochemical Data Set from the O'Grady Pluton, NWT, 1970
orthonorm	Computation of an Orthonormal Basis Matrix

-- R --

remove.na	Remove and Count NAs
rgr	Geological Survey of Canada Applied Geochemistry EDA
rgr-1.1.15	Geological Survey of Canada Applied Geochemistry EDA
rgr_1.1.15	Geological Survey of Canada Applied Geochemistry EDA
rgr_package	Geological Survey of Canada Applied Geochemistry EDA
rng	Undertakes a Range Transformation on the Columns of a Matrix

-- S --

shape	An EDA Graphical Summary
shape.alt	An Alternate EDA Graphical Summary
sind	Sinding-Larsen Norwegian Stream Sediment Test Data Set
sind.mat2open	Sinding-Larsen Norwegian Stream Sediment Test Data Set
syms	Function to Compute the Diameters of Proportional Symbols
syms.pfunc	Function to Demonstrate the Effect of Different Values of p

-- T --

t-test	t-test from Means, Standard Deviations and Sample Sizes
t.test	t-test from Means, Standard Deviations and Sample Sizes
tbplots	Plot Vertical Tukey Boxplots
tbplots.by.var	Plot Vertical Tukey Boxplots for Variables
thplot1	Display a Thompson-Howarth Plot of Duplicate Measurements
thplot2	Display a Thompson-Howarth Plot of Duplicate Measurements, Alternate Input
triples.test1	North American Geochemical Soil Landscapes Project QA/QC data
triples.test2	North American Geochemical Soil Landscapes Project QA/QC data

-- V --

var2fact

Rearranges Data for Variables as Factors

-- W --

where.na	Identify Vector Elements or Data Frame/Matrix Rows with NAs
wtd.sums	Function to Compute Weighted Sums

-- X --

xyplot.eda7	Display a Third Variable in a X-Y Plot using Tukey Boxplot Symbology
xyplot.eda8	Display a Third Variable in a X-Y Plot as Percentiles
xyplot.tags	Display a Plot of Posted Values for a Third Variable
xyplot.z	Display a Third Variable in a X-Y Plot using Proportional Symbols

-- Y --

youden	Estimate the Coefficients of the Reduced Major Axis
youden-plot	Estimate the Coefficients of the Reduced Major Axis
youden.plot	Estimate the Coefficients of the Reduced Major Axis
youden_plot	Estimate the Coefficients of the Reduced Major Axis